Job ID = 2006617 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,270,125 reads read : 1,270,125 reads written : 1,270,125 spots read : 1,197,779 reads read : 1,197,779 reads written : 1,197,779 spots read : 1,324,191 reads read : 1,324,191 reads written : 1,324,191 spots read : 1,191,839 reads read : 1,191,839 reads written : 1,191,839 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529518.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:14 4983934 reads; of these: 4983934 (100.00%) were unpaired; of these: 189028 (3.79%) aligned 0 times 3981919 (79.90%) aligned exactly 1 time 812987 (16.31%) aligned >1 times 96.21% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 4676258 / 4794906 = 0.9753 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 15:36:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 15:36:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:36:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:36:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 15:36:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:36:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:36:26: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:36:26: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:36:26: #1 total tags in treatment: 118648 INFO @ Fri, 05 Jul 2019 15:36:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:36:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:36:26: #1 tags after filtering in treatment: 118648 INFO @ Fri, 05 Jul 2019 15:36:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:36:26: #1 finished! INFO @ Fri, 05 Jul 2019 15:36:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:36:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:36:26: #2 number of paired peaks: 360 WARNING @ Fri, 05 Jul 2019 15:36:26: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Fri, 05 Jul 2019 15:36:26: start model_add_line... INFO @ Fri, 05 Jul 2019 15:36:26: start X-correlation... INFO @ Fri, 05 Jul 2019 15:36:26: end of X-cor INFO @ Fri, 05 Jul 2019 15:36:26: #2 finished! INFO @ Fri, 05 Jul 2019 15:36:26: #2 predicted fragment length is 291 bps INFO @ Fri, 05 Jul 2019 15:36:26: #2 alternative fragment length(s) may be 4,24,53,76,98,136,177,202,254,291,340,364,383,415,486,521,584 bps INFO @ Fri, 05 Jul 2019 15:36:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.05_model.r INFO @ Fri, 05 Jul 2019 15:36:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:36:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:36:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:36:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:36:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:36:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.05_summits.bed INFO @ Fri, 05 Jul 2019 15:36:27: Done! BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:36:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 15:36:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:36:27: #1 read treatment tags... pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:36:27: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:36:27: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:36:27: #1 total tags in treatment: 118648 INFO @ Fri, 05 Jul 2019 15:36:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:36:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:36:27: #1 tags after filtering in treatment: 118648 INFO @ Fri, 05 Jul 2019 15:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:36:27: #1 finished! INFO @ Fri, 05 Jul 2019 15:36:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:36:27: #2 number of paired peaks: 360 WARNING @ Fri, 05 Jul 2019 15:36:27: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Fri, 05 Jul 2019 15:36:27: start model_add_line... INFO @ Fri, 05 Jul 2019 15:36:27: start X-correlation... INFO @ Fri, 05 Jul 2019 15:36:27: end of X-cor INFO @ Fri, 05 Jul 2019 15:36:27: #2 finished! INFO @ Fri, 05 Jul 2019 15:36:27: #2 predicted fragment length is 291 bps INFO @ Fri, 05 Jul 2019 15:36:27: #2 alternative fragment length(s) may be 4,24,53,76,98,136,177,202,254,291,340,364,383,415,486,521,584 bps INFO @ Fri, 05 Jul 2019 15:36:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.10_model.r INFO @ Fri, 05 Jul 2019 15:36:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:36:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:36:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:36:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:36:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:36:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.10_summits.bed INFO @ Fri, 05 Jul 2019 15:36:28: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:36:28: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:36:28: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:36:28: #1 total tags in treatment: 118648 INFO @ Fri, 05 Jul 2019 15:36:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:36:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:36:28: #1 tags after filtering in treatment: 118648 INFO @ Fri, 05 Jul 2019 15:36:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:36:28: #1 finished! INFO @ Fri, 05 Jul 2019 15:36:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:36:28: #2 number of paired peaks: 360 WARNING @ Fri, 05 Jul 2019 15:36:28: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Fri, 05 Jul 2019 15:36:28: start model_add_line... INFO @ Fri, 05 Jul 2019 15:36:28: start X-correlation... INFO @ Fri, 05 Jul 2019 15:36:28: end of X-cor INFO @ Fri, 05 Jul 2019 15:36:28: #2 finished! INFO @ Fri, 05 Jul 2019 15:36:28: #2 predicted fragment length is 291 bps INFO @ Fri, 05 Jul 2019 15:36:28: #2 alternative fragment length(s) may be 4,24,53,76,98,136,177,202,254,291,340,364,383,415,486,521,584 bps INFO @ Fri, 05 Jul 2019 15:36:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.20_model.r INFO @ Fri, 05 Jul 2019 15:36:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:36:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:36:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548163/ERX2548163.20_summits.bed INFO @ Fri, 05 Jul 2019 15:36:29: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling